Carbohydrate‐binding module tribes

Abstract

At present, 69 families of carbohydrate-binding modules (CBMs) have been isolated by statistically significant differences in the amino acid sequences (primary structures) of their members, with most members of different families showing little if any homology. On the other hand, members of the same family have primary and tertiary (three-dimensional) structures that can be computationally aligned, suggesting that they are descended from common protein ancestors. Members of the large majority of CBM families are β-sandwiches. This raises the question of whether members of different families are descended from distant common ancestors, and therefore are members of the same tribe. We have attacked this problem by attempting to computationally superimpose tertiary structure representatives of each of the 53 CBM families that have members with known tertiary structures. When successful, we have aligned locations of secondary structure elements and determined root mean square deviations and percentages of similarity between adjacent amino acid residues in structures from similar families. Further criteria leading to tribal membership are amino acid chain lengths and bound ligands. These considerations have led us to assign 27 families to nine tribes. Eight of the tribes have members with β-sandwich structures, while the ninth is composed of structures with β-trefoils.

Bacterial expansins and related proteins from the world of microbes

“…Support for homology also comes from the similar and unusual ability to induce plant cell wall creep without lytic activity. Moreover, although many classes of CBM have a β-sandwich fold, the specific β-strand arrangement of D2 appears to be unique and is not shared with other CBMs (Carvalho et al 2014). Shoseyov et al (2006) reported that expansin D2 resembles the fold of CBM family 3, but our structural comparison as well as that of Carvalho et al (2014) indicate that D2 has a distinct β-strand arrangement, which makes homology with CBM3 unlikely.…”

“…Moreover, although many classes of CBM have a β-sandwich fold, the specific β-strand arrangement of D2 appears to be unique and is not shared with other CBMs (Carvalho et al 2014). Shoseyov et al (2006) reported that expansin D2 resembles the fold of CBM family 3, but our structural comparison as well as that of Carvalho et al (2014) indicate that D2 has a distinct β-strand arrangement, which makes homology with CBM3 unlikely. Expansin domain D2 is now classified as CBM family 63 in the CAZY.ORG database (Georgelis et al 2012).…”

The unique evolution of the carbohydrate‐binding module CBM20 in laforin

“…In the Carbohydrate Active enZymes (CAZy) database (; http://www.cazy.org/), the SBDs have been classified among the families of carbohydrate‐binding modules (CBMs). Currently, there are 83 different CBM families with 15 considered SBDs due to their ability to bind starch and related α‐glucans, such as glycogen, cyclodextrins and various maltooligosaccharides – these are CBM20, CBM21, CBM25, CBM26, CBM34, CBM41, CBM45, CBM48, CBM53, CBM58, CBM68, CBM69, CBM74, CBM82 and CBM83 . The CBM74 members are about 250 residues long and this family obviously represents a novel type of an SBD .…”

The starch‐binding domain family CBM41—An in silico analysis of evolutionary relationships

“…In general, an SBD is a protein module consisting of ∼100 amino acid residues and containing aromatic residues at certain positions (mostly tryptophans and tyrosines, but also phenylalanines or histidines) that are essential for the SBD to bind carbohydrate, that is, raw starch and/or related α‐glucans, and thus enhance the degradative action of the enzyme to which the SBD is attached . It is of note that raw‐starch degrading amylases without any distinct SBD exist and are also well known .…”